I'm feeling rather foolish.
I have not had any lessons, so had to teach myself. I set the settings on the welder with trial and error until it gave the best results. I know now that I should have been using gas, but didn't know that till today.
The area was prepped very well with everything back to bare metal, although the weld through primer seemed to make it more difficult, so it will undoubtedly be incorrect welder settings (and lack of gas).
I don't have any more welding to do until I get to making engine mounts and modifying the front crossmember. I will definitely get gas for that and practice more.
I'm considering applying the bmw foam sealant stuff in the cavities to improve the situation - what do people think?